They are upgraded versions of the Primagen Trooper and maintain the Primagen's Lightship, mostly around key positions such as the assembly plant computers, or the controls that disable the four force field generators that power the encasement around the ship's Primagen Key.

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Elite Guards are a combination of flesh and machinery that are updated versions of the Primagen Trooper. It is hard to tell what sort of living organism they used to be. While their heads are exposed, they are equipped from shoulder to toe with high-tech armor, which, combined with their incredible height, makes them look quite imposing and terrifying. Their shoulders are protected with large pads, and their arms are also armored. Where their hands should be are two laser blasters. Part of their legs are covered, but their lower legs are protected with a bulkier armor. Their upper and lower torsos, as well their backs, are also covered.

They sport an olive green paint job and a more resilient armor set, making them far more threatening.

The Elite Guards are one of the most devastating enemies encountered in the game, and by any means, the player should never let their guard down for a moment. Alone, an Elite Guard is a dangerous adversary and will tear the player to pieces. Though it wears heavy armor, it can move quite fast and leap from great distances. They also have a cloaking ability at their disposal which they can use to ambush the player. They can attack using laser cannons that come out of their back and can fire multiple plasma projectiles in quick succession. Another of their attacks is focusing energy and firing it off in multiple locations. Their physical attacks consist of a jump attack and melee attacks with their arm cannons. This may cause the player to lose balance and fall to lower levels, forcing the player to traverse to their last location.

When it comes to fighting an Elite Guard in close quarters, it is almost impossible to avoid their attacks, and the player should try to find an open area in which to fight them. If the player is forced to fight them in an enclosed space, it is recommended that they use the Charge Dart Rifle to stun them and follow up with any explosive weaponry at their disposal. If the player encounters an Elite Guard in an open area, they can use the Firestorm Cannon while circle strafing. Use the Cerebral Bore as a last resort.